src/repertoire.r

@@ -1,31 +1,13 @@
 library(immuneSIM)
 
-generate_repertoires <- function(number_of_sequences) {
-  a_chain <- immuneSIM(
-    number_of_seqs = number_of_sequences,
-    species = "hs",
-    receptor = "tr",
-    chain = "a",
-    verbose = TRUE
-  )
-  b_chain <- immuneSIM(
-    number_of_seqs = number_of_sequences,
+sim_repertoire <- immuneSIM(
+  number_of_seqs = 1000,
   species = "hs",
   receptor = "tr",
   chain = "b",
   verbose = TRUE
 )
-  return(list("a_chain" = a_chain, "b_chain" = b_chain))
-}
 
+save(sim_repertoire, file = "data/repertoire")
 
-parse_cli_arguments <- function(args) {
-  if (length(args) != 1) {
-    stop("usage: repertoire.r <number of sequences>")
-  }
-  return(as.integer(args[1]))
-}
-
-args <- commandArgs(trailingOnly = TRUE)
-number_of_sequences <- parse_cli_arguments(args)
-sim_repertoire <- generate_repertoires(number_of_sequences)
+plot_report_repertoire(sim_repertoire, output_dir = "data/reports")